MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux sprite 2.4.20-8 i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2003/10/02 11:50:28.366 TOP_________> 105 705 SET ALNFILE = '1PGV_64.ali' TOP_________> 106 706 SET KNOWNS = '1PGV' TOP_________> 107 707 SET SEQUENCE = '3009' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 TOP_________> 111 711 CALL ROUTINE = 'model' TOP_________> 112 399 CALL ROUTINE = 'getnames' TOP_________> 113 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 114 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 115 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 116 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 117 513 SET ROOT_NAME = SEQUENCE TOP_________> 118 514 RETURN TOP_________> 119 400 CALL ROUTINE = 'homcsr' TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL 1PGV_64.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 4711285 4600.864 4.493 openf5__224_> Open 11 OLD SEQUENTIAL 1PGV_64.ali Read the alignment from file : 1PGV_64.ali Total number of alignment positions: 169 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1PGV 167 1 1PGV 2 3009 166 1 3009 TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1PGV.atm check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE check_a_344_> << END OF COMMAND TOP_________> 122 108 CALL ROUTINE = GENERATE_METHOD TOP_________> 123 77 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS openf5__224_> Open 11 OLD SEQUENTIAL 1PGV_64.ali Dynamically allocated memory at amaxseq [B,kB,MB]: 4555271 4448.507 4.344 openf5__224_> Open 11 OLD SEQUENTIAL 1PGV_64.ali Read the alignment from file : 1PGV_64.ali Total number of alignment positions: 167 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1PGV 167 1 1PGV TOP_________> 124 78 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS openf5__224_> Open 11 OLD SEQUENTIAL 1PGV_64.ali openf5__224_> Open 11 OLD SEQUENTIAL 1PGV_64.ali Read the alignment from file : 1PGV_64.ali Total number of alignment positions: 167 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1PGV 167 1 1PGV TOP_________> 125 79 IF ARGUMENTS = INITIAL_MALIGN3D 0, OPERATION = 'EQ', THEN; = 'GO_TO NO_INITIAL_MALIGN3D' TOP_________> 126 82 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 4711285 4600.864 4.493 openf5__224_> Open 11 OLD SEQUENTIAL 1PGV_64.ali openf5__224_> Open 11 OLD SEQUENTIAL 1PGV_64.ali Read the alignment from file : 1PGV_64.ali Total number of alignment positions: 169 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1PGV 167 1 1PGV 2 3009 166 1 3009 TOP_________> 127 83 READ_TOPOLOGY FILE = TOPLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//top_heav.lib openf5__224_> Open 11 UNKNOWN SEQUENTIAL ${MODINSTALL6v2}/modlib/models.lib TOP_________> 128 84 READ_PARAMETERS FILE = PARLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//par.lib Dynamically allocated memory at amattacns [B,kB,MB]: 4711681 4601.251 4.493 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//par.lib rdparf__232_> parameters BONDS ANGLS DIHEDS IMPROPS MRFP MODE 227 561 661 112 0 0 TOP_________> 129 85 CALL ROUTINE = 'create_topology' TOP_________> 130 100 GENERATE_TOPOLOGY ADD_SEQUENCE = OFF getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 166 atom names : C +N atom indices : 1295 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 166 atom names : C CA +N O atom indices : 1295 1290 0 1296 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 166 1296 1309 0 0 519 patch_______> segment topology patched using RTF: 1 ; ASN ; NTER segments residues atoms bonds angles dihedrals impropers: 1 166 1296 1309 1770 2049 519 iatmcls_286W> MODEL atom not classified: LEU:OT1 LEU iatmcls_286W> MODEL atom not classified: LEU:OT2 LEU patch_______> segment topology patched using RTF: 166 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 1 166 1297 1310 1772 2051 520 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 166 1297 1310 1772 2051 520 TOP_________> 131 101 CALL ROUTINE = 'default_patches' TOP_________> 132 504 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE openf5__224_> Open 11 OLD SEQUENTIAL 1PGV_64.ali openf5__224_> Open 11 OLD SEQUENTIAL 1PGV_64.ali Read the alignment from file : 1PGV_64.ali Total number of alignment positions: 169 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1PGV 167 1 1PGV 2 3009 166 1 3009 TOP_________> 133 505 PATCH_SS_TEMPLATES TOP_________> 134 506 RETURN TOP_________> 135 102 CALL ROUTINE = 'special_patches' TOP_________> 136 501 RETURN TOP_________> 137 103 RETURN TOP_________> 138 86 TRANSFER_XYZ CLUSTER_CUT = -1.0 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 1 After transfering coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 1062 235 TOP_________> 139 87 BUILD_MODEL INITIALIZE_XYZ = OFF TOP_________> 140 88 WRITE_MODEL FILE = MODEL openf5__224_> Open 14 UNKNOWN SEQUENTIAL 3009.ini wrpdb2__568_> Residues, atoms, selected atoms: 166 1297 1297 TOP_________> 141 89 RETURN TOP_________> 142 109 IF ARGUMENTS = EXIT_STAGE 2, OPERATION = 'EQ', THEN = 'RE; TURN' TOP_________> 143 110 IF ARGUMENTS = CREATE_RESTRAINTS 0, OPERATION = 'EQ', THE; N ='GO_TO __SKIP_RSRS' TOP_________> 144 111 CALL ROUTINE = 'mkhomcsr' TOP_________> 145 116 MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo', ADD_RESTRAINTS; = OFF Dynamically allocated memory at amprmcns [B,kB,MB]: 11015953 10757.770 10.506 make_re_417_> Restraint type to be calculated: stereo r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 1310 1772 1933 514 Total number of restraints before, now : 0 5529 make_re_422_> Number of previous, current restraints : 0 5529 make_re_423_> Number of previous, current selected restraints: 0 5529 TOP_________> 146 117 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE openf5__224_> Open 11 OLD SEQUENTIAL 1PGV_64.ali openf5__224_> Open 11 OLD SEQUENTIAL 1PGV_64.ali Read the alignment from file : 1PGV_64.ali Total number of alignment positions: 169 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1PGV 167 1 1PGV 2 3009 166 1 3009 TOP_________> 147 118 MAKE_RESTRAINTS RESTRAINT_TYPE = 'phi-psi_binormal', ADD_; RESTRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 11015953 10757.770 10.506 make_re_417_> Restraint type to be calculated: phi-psi_binormal openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mnch1.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mnch1.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. getdata_643_> Protein accepted: 1PGV getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 5529 5693 make_re_423_> Number of previous, current selected restraints: 5529 5693 TOP_________> 148 119 SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.3, SPLINE_MIN_POINT; S = 5 TOP_________> 149 120 MAKE_RESTRAINTS RESTRAINT_TYPE = 'omega_dihedral', ADD_RE; STRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 11015953 10757.770 10.506 make_re_417_> Restraint type to be calculated: omega_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/omega.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/omega.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. getdata_643_> Protein accepted: 1PGV getdata_289_> Proteins (all/accepted): 1 1 omgdel__425W> Unselected all O C +N +CA dihedrals: 171 make_re_422_> Number of previous, current restraints : 5693 5858 make_re_423_> Number of previous, current selected restraints: 5693 5687 TOP_________> 150 121 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi1_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 11015953 10757.770 10.506 make_re_417_> Restraint type to be calculated: chi1_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi1.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. getdata_643_> Protein accepted: 1PGV getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 5858 6007 make_re_423_> Number of previous, current selected restraints: 5687 5836 TOP_________> 151 122 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi2_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 11015953 10757.770 10.506 make_re_417_> Restraint type to be calculated: chi2_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi2.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. getdata_643_> Protein accepted: 1PGV getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 6007 6122 make_re_423_> Number of previous, current selected restraints: 5836 5951 TOP_________> 152 123 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi3_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 11015953 10757.770 10.506 make_re_417_> Restraint type to be calculated: chi3_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi3.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. getdata_643_> Protein accepted: 1PGV getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 6122 6170 make_re_423_> Number of previous, current selected restraints: 5951 5999 TOP_________> 153 124 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi4_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 11015953 10757.770 10.506 make_re_417_> Restraint type to be calculated: chi4_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi4.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. getdata_643_> Protein accepted: 1PGV getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 6170 6188 make_re_423_> Number of previous, current selected restraints: 5999 6017 TOP_________> 154 125 SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.7, SPLINE_MIN_POINT; S = 5 TOP_________> 155 126 SET RES_TYPES = 'STD' TOP_________> 156 127 SET DISTANCE_RSR_MODEL = 5, MAXIMAL_DISTANCE = MAX_CA-CA_; DISTANCE TOP_________> 157 128 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON TOP_________> 158 129 SET RESTRAINT_GROUP = 9 TOP_________> 159 130 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 1297 1297 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 166 1: 166: selatm__462_> Number of selected atoms : 166 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : ASN --- 166 : LEU 166 TOP_________> 160 131 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 1297 1297 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 166 1: 166: selatm__462_> Number of selected atoms : 166 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : ASN --- 166 : LEU 166 TOP_________> 161 132 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 11015953 10757.770 10.506 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 6188 9380 make_re_423_> Number of previous, current selected restraints: 6017 9209 TOP_________> 162 133 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_N-O_DI; STANCE TOP_________> 163 134 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 164 135 SET RESTRAINT_GROUP = 10 TOP_________> 165 136 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'N' Number of atoms to choose from, total : 1297 1297 Atom types to be searched for (ATOM_TYPES) : N Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 166 1: 166: selatm__462_> Number of selected atoms : 166 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : ASN --- 166 : LEU 166 TOP_________> 166 137 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'O' Number of atoms to choose from, total : 1297 1297 Atom types to be searched for (ATOM_TYPES) : O Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 166 1: 166: selatm__462_> Number of selected atoms : 166 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : ASN --- 166 : LEU 166 TOP_________> 167 138 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 11015953 10757.770 10.506 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 9380 12786 make_re_423_> Number of previous, current selected restraints: 9209 12615 TOP_________> 168 139 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-MC_; DISTANCE TOP_________> 169 140 SET RESIDUE_SPAN_RANGE = 1 2, RESIDUE_SPAN_SIGN = OFF TOP_________> 170 141 SET RESTRAINT_GROUP = 23, RESTRAINT_STDEV = 0.5 1.5 TOP_________> 171 142 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 1297 1297 Atom types to be searched for (ATOM_TYPES) : SDCH Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 166 1: 166: selatm__462_> Number of selected atoms : 632 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : ASN --- 54 : VAL 54 2 56 : THR --- 87 : SER 32 3 89 : SER --- 89 : SER 1 4 91 : ILE --- 116 : LEU 26 5 118 : ASN --- 137 : PHE 20 6 139 : TYR --- 144 : GLN 6 7 146 : PRO --- 166 : LEU 21 TOP_________> 172 143 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'MNCH' Number of atoms to choose from, total : 1297 1297 Atom types to be searched for (ATOM_TYPES) : MNCH Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 166 1: 166: selatm__462_> Number of selected atoms : 665 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : ASN --- 166 : LEU 166 TOP_________> 173 144 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 11015953 10757.770 10.506 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 12786 14575 make_re_423_> Number of previous, current selected restraints: 12615 14404 TOP_________> 174 145 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-SC_; DISTANCE TOP_________> 175 146 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON TOP_________> 176 147 SET RESTRAINT_GROUP = 26, RESTRAINT_STDEV = 0.5 2.0 TOP_________> 177 148 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 1297 1297 Atom types to be searched for (ATOM_TYPES) : SDCH Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 166 1: 166: selatm__462_> Number of selected atoms : 632 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : ASN --- 54 : VAL 54 2 56 : THR --- 87 : SER 32 3 89 : SER --- 89 : SER 1 4 91 : ILE --- 116 : LEU 26 5 118 : ASN --- 137 : PHE 20 6 139 : TYR --- 144 : GLN 6 7 146 : PRO --- 166 : LEU 21 TOP_________> 178 149 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 1297 1297 Atom types to be searched for (ATOM_TYPES) : SDCH Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 166 1: 166: selatm__462_> Number of selected atoms : 632 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : ASN --- 54 : VAL 54 2 56 : THR --- 87 : SER 32 3 89 : SER --- 89 : SER 1 4 91 : ILE --- 116 : LEU 26 5 118 : ASN --- 137 : PHE 20 6 139 : TYR --- 144 : GLN 6 7 146 : PRO --- 166 : LEU 21 TOP_________> 179 150 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 11015953 10757.770 10.506 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 14575 15079 make_re_423_> Number of previous, current selected restraints: 14404 14908 TOP_________> 180 151 CALL ROUTINE = 'hetatm_restraints' TOP_________> 181 160 SET RESTRAINT_TYPE = 'distance' TOP_________> 182 161 SET DISTANCE_RSR_MODEL = 7 TOP_________> 183 162 SET MAXIMAL_DISTANCE = 7.0 TOP_________> 184 163 SET ADD_RESTRAINTS = ON TOP_________> 185 164 SET RESTRAINT_GROUP = 27 TOP_________> 186 165 SET RESTRAINT_STDEV = 0.2 0.0 TOP_________> 187 166 SET RESIDUE_SPAN_RANGE = 0 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 188 167 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_TY; PES = 'ALL' Number of atoms to choose from, total : 1297 1297 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : ALL Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 166 1: 166: selatm__462_> Number of selected atoms : 1297 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : ASN --- 166 : LEU 166 TOP_________> 189 168 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'HET' Number of atoms to choose from, total : 1297 1297 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : HET Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 166 1: 166: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 190 169 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 11015953 10757.770 10.506 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 15079 15079 make_re_423_> Number of previous, current selected restraints: 14908 14908 TOP_________> 191 170 RETURN TOP_________> 192 152 CALL ROUTINE = 'blk_restraints' TOP_________> 193 173 SET RESTRAINT_TYPE = 'distance' TOP_________> 194 174 SET DISTANCE_RSR_MODEL = 7 TOP_________> 195 175 SET MAXIMAL_DISTANCE = 10.0 TOP_________> 196 176 SET ADD_RESTRAINTS = ON TOP_________> 197 177 SET RESTRAINT_GROUP = 27 TOP_________> 198 178 SET RESTRAINT_STDEV = 0.05 0.0 TOP_________> 199 179 SET RESIDUE_SPAN_RANGE = 0 0, RESIDUE_SPAN_SIGN = ON TOP_________> 200 180 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_T; YPES = 'BLK' Number of atoms to choose from, total : 1297 1297 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : BLK Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 166 1: 166: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 201 181 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_T; YPES = 'BLK' Number of atoms to choose from, total : 1297 1297 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : BLK Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 166 1: 166: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 202 182 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 11015953 10757.770 10.506 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 15079 15079 make_re_423_> Number of previous, current selected restraints: 14908 14908 TOP_________> 203 183 SET RESTRAINT_STDEV = 0.2 0.0 TOP_________> 204 184 SET RESIDUE_SPAN_RANGE = 1 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 205 185 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA', RES_TY; PES = 'ALL' Number of atoms to choose from, total : 1297 1297 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : ALL Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 166 1: 166: selatm__462_> Number of selected atoms : 166 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : ASN --- 166 : LEU 166 TOP_________> 206 186 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'BLK' Number of atoms to choose from, total : 1297 1297 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : BLK Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 166 1: 166: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 207 187 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 11015953 10757.770 10.506 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 15079 15079 make_re_423_> Number of previous, current selected restraints: 14908 14908 TOP_________> 208 188 DELETE_ALIGNMENT TOP_________> 209 189 RETURN Dynamically allocated memory at amaxseq [B,kB,MB]: 10859939 10605.410 10.357 TOP_________> 210 153 CALL ROUTINE = 'special_restraints' TOP_________> 211 498 RETURN TOP_________> 212 154 CONDENSE_RESTRAINTS delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 15079 13891 TOP_________> 213 155 WRITE_RESTRAINTS FILE = CSRFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL 3009.rsr TOP_________> 214 156 SET RESIDUE_SPAN_RANGE = -999 -999, RESIDUE_SPAN_SIGN = O; N TOP_________> 215 157 RETURN TOP_________> 216 112 LABEL __SKIP_RSRS TOP_________> 217 113 RETURN TOP_________> 218 401 IF ARGUMENTS = EXIT_STAGE 1, OPERATION = 'GE', THEN = 'RE; TURN' TOP_________> 219 402 CALL ROUTINE = 'rd_restraints' TOP_________> 220 255 READ_RESTRAINTS FILE = CSRFILE, ADD_RESTRAINTS = 'off' openf5__224_> Open 11 OLD SEQUENTIAL 3009.rsr openf5__224_> Open 11 OLD SEQUENTIAL 3009.rsr rdcsr2__307_> Number of restraints read : 0 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 Dynamically allocated memory at amprmcns [B,kB,MB]: 10859939 10605.410 10.357 openf5__224_> Open 11 OLD SEQUENTIAL 3009.rsr openf5__224_> Open 11 OLD SEQUENTIAL 3009.rsr rdcsr2__307_> Number of restraints read : 0 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 13891 13891 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 TOP_________> 221 256 RETURN TOP_________> 222 403 CALL ROUTINE = 'multiple_models' TOP_________> 223 192 DO ID2 = STARTING_MODEL ENDING_MODEL 1 TOP_________> 224 193 SET FINAL_MODEL = 'default' TOP_________> 225 194 CALL ROUTINE = 'single_model' TOP_________> 226 205 SET MAX_ITERATIONS = MAX_VAR_ITERATIONS TOP_________> 227 206 SET ID1 = 0 TOP_________> 228 207 SWITCH_TRACE FILE = 'default', FILE_EXT = '', FILE_ID = '; .D' openf5__224_> Open 18 UNKNOWN SEQUENTIAL 3009.D00000001 TOP_________> 229 208 READ_MODEL FILE = MODEL openf5__224_> Open 11 OLD SEQUENTIAL 3009.ini openf5__224_> Open 11 OLD SEQUENTIAL 3009.ini rdatm___297_> Segments, residues, atoms: 1 166 1297 rdatm___298_> Segment: 1 1 1 1297 iatmcls_286W> MODEL atom not classified: LEU:OT1 LEU iatmcls_286W> MODEL atom not classified: LEU:OT2 LEU TOP_________> 230 209 CALL ROUTINE = 'select_atoms' TOP_________> 231 267 PICK_ATOMS SELECTION_SEGMENT ='@:@' 'X:X', SELECTION_SEAR; CH ='segment', PICK_ATOMS_SET =1, RES_TYPES =; 'all', ATOM_TYPES ='all', SELECTION_FROM ='a; ll', SELECTION_STATUS ='initialize' Number of atoms to choose from, total : 1297 1297 Atom types to be searched for (ATOM_TYPES) : all Residue types to be searched for (RES_TYPES) : all Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): initialize SEGMENT search; residue range (2i5,2a5) : 1 166 1: 166: selatm__462_> Number of selected atoms : 1297 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : ASN --- 166 : LEU 166 TOP_________> 232 268 RETURN TOP_________> 233 210 CALL ROUTINE = RAND_METHOD TOP_________> 234 251 RANDOMIZE_XYZ randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1297 1297 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. TOP_________> 235 252 RETURN TOP_________> 236 211 MAKE_SCHEDULE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/sched.lib TOP_________> 237 212 WRITE_SCHEDULE FILE = SCHFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL 3009.sch TOP_________> 238 213 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = PDB_E; XT', FILE_ID = '.B' TOP_________> 239 214 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1 TOP_________> 240 215 CALL ROUTINE = 'single_model_pass' TOP_________> 241 231 DO SCHEDULE_STEP = 1 N_SCHEDULE 1 TOP_________> 242 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 243 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 1297 7330 TOP_________> 244 234 OPTIMIZE Dynamically allocated memory at ampairs [B,kB,MB]: 11042805 10783.990 10.531 TOP_________> 245 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 246 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 247 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 248 238 END_DO TOP_________> 249 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 250 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 1297 8271 TOP_________> 251 234 OPTIMIZE TOP_________> 252 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 253 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 254 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 255 238 END_DO TOP_________> 256 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 257 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 1297 8822 TOP_________> 258 234 OPTIMIZE TOP_________> 259 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 260 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 261 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 262 238 END_DO TOP_________> 263 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 264 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 1297 9360 TOP_________> 265 234 OPTIMIZE TOP_________> 266 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 267 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 268 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 269 238 END_DO TOP_________> 270 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 271 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 1297 9955 TOP_________> 272 234 OPTIMIZE TOP_________> 273 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 274 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 275 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 276 238 END_DO TOP_________> 277 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 278 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 1297 12552 TOP_________> 279 234 OPTIMIZE TOP_________> 280 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 281 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 282 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 283 238 END_DO TOP_________> 284 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 285 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 1297 13455 TOP_________> 286 234 OPTIMIZE TOP_________> 287 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 288 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 289 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 290 238 END_DO TOP_________> 291 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 292 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 1297 13876 TOP_________> 293 234 OPTIMIZE TOP_________> 294 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 295 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 296 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 297 238 END_DO TOP_________> 298 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 299 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 1297 13891 TOP_________> 300 234 OPTIMIZE TOP_________> 301 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 302 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 303 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 304 238 END_DO TOP_________> 305 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 306 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 1297 13891 TOP_________> 307 234 OPTIMIZE TOP_________> 308 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 309 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 310 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 311 238 END_DO TOP_________> 312 239 CALL ROUTINE = 'refine', SCHEDULE_STEP = N_SCHEDULE TOP_________> 313 271 STRING_IF STRING_ARGUMENTS = MD_LEVEL 'none', OPERATION =; 'EQ', THEN = RETURN TOP_________> 314 272 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'NE', THEN = 'WRITE_MODEL FILE = TO_BE_REFIN; ED.TMP' TOP_________> 315 273 SET MAX_ITERATIONS_STORE = MAX_ITERATIONS TOP_________> 316 274 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __BEGIN_MD' TOP_________> 317 285 CALL ROUTINE = MD_LEVEL TOP_________> 318 310 SET UPDATE_DYNAMIC = 0.39 TOP_________> 319 311 SET CAP_ATOM_SHIFT = UPDATE_DYNAMIC, MD_TIME_STEP = 4.0 TOP_________> 320 312 SET MAX_ITERATIONS = 50, EQUILIBRATE = 10, OPTIMIZATION_M; ETHOD = 3 TOP_________> 321 313 OPTIMIZE TEMPERATURE = 150.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = ON TOP_________> 322 314 OPTIMIZE TEMPERATURE = 400.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = OFF TOP_________> 323 315 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 324 316 SET EQUILIBRATE = 100, MAX_ITERATIONS = 300 TOP_________> 325 317 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 326 318 OPTIMIZE TEMPERATURE = 800.0, MD_RETURN = 'FINAL' TOP_________> 327 319 OPTIMIZE TEMPERATURE = 500.0, MD_RETURN = 'FINAL' TOP_________> 328 320 OPTIMIZE TEMPERATURE = 300.0, MD_RETURN = 'FINAL' TOP_________> 329 321 RETURN TOP_________> 330 286 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __AFTER_MD' TOP_________> 331 291 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200 TOP_________> 332 292 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'INDEX', THEN = 'GO_TO __NO_FIT' TOP_________> 333 306 SET MAX_ITERATIONS = MAX_ITERATIONS_STORE TOP_________> 334 307 RETURN TOP_________> 335 240 LABEL __ABORT TOP_________> 336 241 SET ERROR_STATUS = 0 TOP_________> 337 242 RETURN TOP_________> 338 216 END_DO TOP_________> 339 217 IUPAC_MODEL iupac_m_485_> OD1/2 swapped: 131.8291 18 18 iupac_m_487_> NH1/2 swapped: -178.2390 57 57 iupac_m_486_> OE1/2 swapped: -164.7577 82 82 iupac_m_487_> NH1/2 swapped: 178.5486 108 108 iupac_m_487_> NH1/2 swapped: 178.8114 149 149 iupac_m_487_> NH1/2 swapped: 179.6221 164 164 TOP_________> 340 218 SET ID1 = 9999 TOP_________> 341 219 SET OUTPUT2 = OUTPUT TOP_________> 342 220 ENERGY OUTPUT = 'LONG VIOLATIONS_PROFILE', FILE = 'defaul; t', FILE_ID = '.V', FILE_EXT = '' >> ENERGY; Differences between the model's features and restraints: ID1, ID2 : 9999 1 Number of all residues in MODEL : 166 Number of all, selected real atoms : 1297 1297 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 13891 13891 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3109 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 200 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SCHEDULE_STEP, N_SCHEDULE : 10 10 SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 886.5582 Symmetry term within energy : 0.0000 Summary of the restraint violations: NUM ... number of restraints. NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. RVIOL ... relative difference from the best value. NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). RMS_2 ... RMS(feature, best_value, NUMB). MOL.PDF ... scaled contribution to -Ln(Molecular pdf). # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 1 Bond length potential : 1310 0 0 0.006 0.006 11.516 1.000 2 Bond angle potential : 1772 0 9 2.158 2.158 163.74 1.000 3 Stereochemical cosine torsion poten: 745 0 29 49.741 49.741 287.21 1.000 4 Stereochemical improper torsion pot: 514 0 0 1.307 1.307 20.593 1.000 5 Soft-sphere overlap restraints : 3109 0 0 0.002 0.002 1.2498 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.00000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.00000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.00000 1.000 9 Distance restraints 1 (CA-CA) : 3192 0 0 0.178 0.178 59.369 1.000 10 Distance restraints 2 (N-O) : 3406 1 10 0.248 0.248 134.59 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.00000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.00000 1.000 13 Mainchain Omega dihedral restraints: 165 0 1 4.689 4.689 42.790 1.000 14 Sidechain Chi_1 dihedral restraints: 149 0 0 69.118 69.118 23.274 1.000 15 Sidechain Chi_2 dihedral restraints: 115 0 0 70.376 70.376 45.459 1.000 16 Sidechain Chi_3 dihedral restraints: 48 0 0 76.986 76.986 34.631 1.000 17 Sidechain Chi_4 dihedral restraints: 18 0 0 112.148 112.148 14.835 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.00000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.00000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.00000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.00000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.00000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 1789 0 0 0.295 0.295 22.101 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.00000 1.000 25 Phi/Psi pair of dihedral restraints: 164 4 13 21.716 34.352 -3.9264 1.000 26 Distance restraints 4 (SDCH-SDCH) : 504 0 0 0.736 0.736 29.132 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.00000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.00000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.00000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.00000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.00000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.00000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.00000 1.000 openf5__224_> Open 17 UNKNOWN SEQUENTIAL 3009.V99990001 # Heavy relative violation of each residue is written to: 3009.V99990001 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 10 : Distance restraints 2 (N-O) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 11285 148L 144Q N O 1141 1118 5.61 2.90 2.70 4.68 2.90 2.70 4.68 ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 4342 1N 2S C N 7 9 -87.40 -72.40 25.30 1.16 -64.10 154.00 12.69 1 2S 2S N CA 9 10 172.77 152.40 -35.00 2 4455 114Q 115P C N 874 876 -78.06 -64.50 25.81 1.50 -58.70 161.51 14.94 2 115P 115P N CA 876 877 169.16 147.20 -30.50 3 4484 143Q 144Q C N 1108 1110 -74.13 -121.10 47.78 1.98 -63.80 171.56 25.77 3 144Q 144Q N CA 1110 1111 148.45 139.70 -40.30 4 4485 144Q 145G C N 1117 1119 105.45 82.20 75.99 2.55 -62.40 169.37 29.25 4 145G 145G N CA 1119 1120 -63.85 8.50 -41.20 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 14 23 77 117 161 136 179 223 235 254 << end of ENERGY. TOP_________> 343 221 SET OUTPUT = OUTPUT2 TOP_________> 344 222 CALL ROUTINE = 'user_after_single_model' TOP_________> 345 228 RETURN TOP_________> 346 223 WRITE_MODEL FILE = FINAL_MODEL, FILE_ID = '.B', FILE_EXT ; = PDB_EXT openf5__224_> Open 14 UNKNOWN SEQUENTIAL 3009.B99990001 wrpdb2__568_> Residues, atoms, selected atoms: 166 1297 1297 TOP_________> 347 224 SET FINAL_MODEL = FILE TOP_________> 348 225 RETURN TOP_________> 349 195 END_DO TOP_________> 350 196 IF ARGUMENTS = DO_LOOPS 1, OPERATION = 'NE', THEN = 'GO_T; O NO_LOOPS' TOP_________> 351 202 RETURN TOP_________> 352 404 IF ARGUMENTS =FINAL_MALIGN3D 1, OPERATION ='NE', THEN ='G; O_TO NO_MALIGN3D' TOP_________> 353 411 RETURN Dynamically allocated memory at finish [B,kB,MB]: 11042805 10783.990 10.531 Starting time : 2003/10/02 11:50:28.366 Closing time : 2003/10/02 11:51:26.741 Total CPU time [seconds] : 58.02